Mercurial > repos > earlhaminst > lotus2
changeset 12:3f3ee496acec draft
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a"
| author | earlhaminst |
|---|---|
| date | Wed, 09 Jun 2021 15:55:53 +0000 |
| parents | 8f732780e0f3 |
| children | f2bb89058e99 |
| files | lotus2.xml |
| diffstat | 1 files changed, 18 insertions(+), 2 deletions(-) [+] |
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--- a/lotus2.xml Tue Jun 08 19:53:13 2021 +0000 +++ b/lotus2.xml Wed Jun 09 15:55:53 2021 +0000 @@ -41,8 +41,24 @@ <command detect_errors="exit_code"><![CDATA[ #import os.path #import re -#def symlink_basename($f): +#def symlink_basename($f, strip_ext=False): #set $fn = re.sub('[^\w\-_.]', '_', $f.name) + #if strip_ext: + #if $fn.endswith('.gz'): + #set $fn = $fn[:-3] + #end if + #if $f.ext.startswith('fasta'): + #set $exts_to_drop = ('.fa', '.fasta', '.fna') + #else: + #set $exts_to_drop = [] + #end if + #for $ext in $exts_to_drop: + #if $fn.endswith($ext): + #set $fn = $fn[:-len($ext)] + #break + #end if + #end for + #end if ${fn}#slurp #end def @@ -61,7 +77,7 @@ #if $tax_args.aligner_cond.taxAligner not in ('0', '3') and $tax_args.aligner_cond.refDB_cond.refDB == 'history': #set $ext = $tax_args.aligner_cond.refDB_cond.ref_fasta.ext - #set $ref_fasta_symlink = $symlink_basename($tax_args.aligner_cond.refDB_cond.ref_fasta, $ext) + '.' + $ext + #set $ref_fasta_symlink = $symlink_basename($tax_args.aligner_cond.refDB_cond.ref_fasta, strip_ext=True) + '.' + $ext ln -s '$tax_args.aligner_cond.refDB_cond.ref_fasta' '$ref_fasta_symlink' && #end if